+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ec7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of SdgB (complexed with phosphate ions) | ||||||||||||
![]() | Glycosyl transferase, group 1 family protein | ||||||||||||
![]() | TRANSFERASE / Glycosylation | ||||||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / cytoplasm / PHOSPHATE ION / Glycosyl transferase, group 1 family protein![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Authors: Kim, D.G. / Baek, I. / Lee, Y. / Kim, H. / Kim, J.Y. / Bang, G. / Kim, S. / Yoon, H.J. / Han, B.W. / Suh, S.W. / Kim, H.S. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 213.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 172 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ec1SC ![]() 7ec3C ![]() 7ec6C ![]() 7vfkC ![]() 7vflC ![]() 7vfmC ![]() 7vfnC ![]() 7vfoC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 59888.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USA300 / Gene: SAUSA300_0550 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.78 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 1.2 M NaH2PO4, 0.8 M K2HPO4, and 0.1 M CAPS-NaOH (pH 10.5) |
-Data collection
Diffraction | Mean temperature: 287 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 26949 / % possible obs: 89 % / Redundancy: 8.2 % / CC1/2: 0.973 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 3.2→3.26 Å / Num. unique obs: 1492 / CC1/2: 0.916 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7EC1 Resolution: 3.2→29.98 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.958 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.13 Å2 / Biso mean: 60.717 Å2 / Biso min: 18.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→29.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|